def apply_my_filters(s):
s = default_filters(s)
s = add_parent_mass(s)
s = normalize_intensities(s)
s = select_by_relative_intensity(s, intensity_from=0.0, intensity_to=1.0)
s = select_by_mz(s, mz_from=0, mz_to=1000)
s = require_minimum_number_of_peaks(s, n_required=5)
return s
def test_add_parent_mass_not_sufficient_data(caplog):
"""Test when there is not enough information to derive parent_mass."""
metadata = {"precursor_mz": 444.0}
spectrum_in = SpectrumBuilder().with_metadata(metadata).build()
spectrum = add_parent_mass(spectrum_in)
assert spectrum.get("parent_mass") is None, "Expected no parent mass"
assert "Not sufficient spectrum metadata to derive parent mass." in caplog.text
def test_use_of_ionmode(ionmode, expected):
"""Test when there is no charge given, than the ionmode
is used to derive parent mass."""
metadata = {"precursor_mz": 444.0, "ionmode": ionmode}
spectrum_in = SpectrumBuilder().with_metadata(metadata).build()
spectrum = add_parent_mass(spectrum_in)
assert spectrum.get("parent_mass") == expected, \
"Expected a different parent_mass"
def test_add_parent_mass():
"""Test if parent mass is correctly derived."""
mz = numpy.array([], dtype='float')
intensities = numpy.array([], dtype='float')
metadata = {"pepmass": (444.0, 10), "charge": -1}
spectrum_in = Spectrum(mz=mz, intensities=intensities, metadata=metadata)
spectrum = add_parent_mass(spectrum_in)
assert numpy.abs(spectrum.get("parent_mass") -
445.0) < .01, "Expected parent mass of about 445.0."
def test_add_parent_mass_using_adduct(adduct, expected):
"""Test if parent mass is correctly derived from adduct information."""
metadata = {"precursor_mz": 444.0, "adduct": adduct, "charge": +1}
spectrum_in = SpectrumBuilder().with_metadata(metadata).build()
spectrum = add_parent_mass(spectrum_in)
assert numpy.allclose(
spectrum.get("parent_mass"), expected,
atol=1e-4), f"Expected parent mass of about {expected}."
assert isinstance(spectrum.get("parent_mass"),
float), "Expected parent mass to be float."
def test_add_parent_mass_precursormz(caplog):
"""Test if parent mass is correctly derived if "pepmass" is not present."""
metadata = {"precursor_mz": 444.0, "charge": -1}
spectrum_in = SpectrumBuilder().with_metadata(metadata).build()
spectrum = add_parent_mass(spectrum_in)
assert numpy.abs(spectrum.get("parent_mass") -
445.0) < .01, "Expected parent mass of about 445.0."
assert isinstance(spectrum.get("parent_mass"),
float), "Expected parent mass to be float."
assert "Not sufficient spectrum metadata to derive parent mass." not in caplog.text
def apply_my_filters(s):
"""This is how a user would typically design his own pre- and post-
processing pipeline."""
s = default_filters(s)
s = add_parent_mass(s)
s = normalize_intensities(s)
s = reduce_to_number_of_peaks(s, n_required=10, ratio_desired=0.5)
s = select_by_mz(s, mz_from=0, mz_to=1000)
s = add_losses(s, loss_mz_from=10.0, loss_mz_to=200.0)
s = require_minimum_number_of_peaks(s, n_required=5)
return s
def test_add_parent_mass_using_adduct(adduct, expected):
"""Test if parent mass is correctly derived from adduct information."""
mz = numpy.array([], dtype='float')
intensities = numpy.array([], dtype='float')
metadata = {"precursor_mz": 444.0, "adduct": adduct, "charge": +1}
spectrum_in = Spectrum(mz=mz, intensities=intensities, metadata=metadata)
spectrum = add_parent_mass(spectrum_in)
assert numpy.allclose(
spectrum.get("parent_mass"), expected,
atol=1e-4), f"Expected parent mass of about {expected}."
def test_add_parent_mass_not_sufficient_data(capsys):
"""Test when there is not enough information to derive parent_mass."""
mz = numpy.array([], dtype='float')
intensities = numpy.array([], dtype='float')
metadata = {"precursor_mz": 444.0}
spectrum_in = Spectrum(mz=mz, intensities=intensities, metadata=metadata)
spectrum = add_parent_mass(spectrum_in)
assert spectrum.get("parent_mass") is None, "Expected no parent mass"
assert "Not sufficient spectrum metadata to derive parent mass." in capsys.readouterr(
).out
def test_add_parent_mass_no_pepmass(capsys):
"""Test if correct expection is returned."""
mz = numpy.array([], dtype='float')
intensities = numpy.array([], dtype='float')
metadata = {"charge": -1}
spectrum_in = Spectrum(mz=mz, intensities=intensities, metadata=metadata)
spectrum = add_parent_mass(spectrum_in)
assert spectrum.get("parent_mass") is None, "Expected no parent mass"
assert "Not sufficient spectrum metadata to derive parent mass." in capsys.readouterr(
).out
def test_add_parent_mass_overwrite(overwrite, expected):
"""Test if parent mass is replaced by newly calculated value."""
metadata = {
"precursor_mz": 444.0,
"parent_mass": 443.0,
"adduct": "[M+H]+",
"charge": +1
}
spectrum_in = SpectrumBuilder().with_metadata(metadata).build()
spectrum = add_parent_mass(spectrum_in, overwrite_existing_entry=overwrite)
assert numpy.allclose(spectrum.get("parent_mass"), expected, atol=1e-4), \
"Expected parent mass to be replaced by new value."
def test_add_parent_mass(capsys):
"""Test if parent mass is correctly derived."""
mz = numpy.array([], dtype='float')
intensities = numpy.array([], dtype='float')
metadata = {"pepmass": (444.0, 10), "charge": -1}
spectrum_in = Spectrum(mz=mz, intensities=intensities, metadata=metadata)
spectrum = add_parent_mass(spectrum_in)
assert numpy.abs(spectrum.get("parent_mass") -
445.0) < .01, "Expected parent mass of about 445.0."
assert isinstance(spectrum.get("parent_mass"),
float), "Expected parent mass to be float."
assert "Not sufficient spectrum metadata to derive parent mass." not in capsys.readouterr(
).out
def test_add_parent_mass_overwrite():
"""Test if parent mass is replaced by newly calculated value."""
mz = numpy.array([], dtype='float')
intensities = numpy.array([], dtype='float')
metadata = {
"precursor_mz": 444.0,
"parent_mass": 443.0,
"adduct": "[M+H]+",
"charge": +1
}
spectrum_in = Spectrum(mz=mz, intensities=intensities, metadata=metadata)
spectrum = add_parent_mass(spectrum_in, overwrite_existing_entry=True)
assert numpy.allclose(spectrum.get("parent_mass"), 442.992724, atol=1e-4), \
"Expected parent mass to be replaced by new value."
def test_empty_spectrum():
spectrum_in = None
spectrum = add_parent_mass(spectrum_in)
assert spectrum is None, "Expected different handling of None spectrum."
def test_add_parent_mass_exceptions(metadata, expected, caplog):
spectrum_in = SpectrumBuilder().with_metadata(metadata).build()
spectrum = add_parent_mass(spectrum_in)
assert spectrum.get("parent_mass") is None, "Expected no parent mass"
assert expected in caplog.text
